Scn11a (sodium channel, voltage-gated, type XI, alpha) - Rat Genome Database

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Gene: Scn11a (sodium channel, voltage-gated, type XI, alpha) Mus musculus
Analyze
Symbol: Scn11a
Name: sodium channel, voltage-gated, type XI, alpha
RGD ID: 735313
MGI Page MGI
Description: Exhibits voltage-gated sodium channel activity. Involved in regulation of sensory perception of pain and sodium ion transport. Localizes to C-fiber and plasma membrane. Is expressed in several structures, including alimentary system; central nervous system; immune system; liver and biliary system; and reproductive system. Used to study familial episodic pain syndrome 3 and hereditary sensory neuropathy. Human ortholog(s) of this gene implicated in familial episodic pain syndrome 3 and hereditary sensory and autonomic neuropathy type 7. Orthologous to human SCN11A (sodium voltage-gated channel alpha subunit 11); INTERACTS WITH 1,2-dichloroethane; 2,3,7,8-tetrachlorodibenzodioxine; pirinixic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: N; NaN; NaT; NaV1.9; NSS2; S; sensory neuron sodium channel 2; SNS2; sodium channel protein type 11 subunit alpha; sodium channel protein type XI subunit alpha; sodium channel, voltage-gated, type XI, alpha polypeptide; voltage-gated sodium channel Nav1.9 variant a; voltage-gated sodium channel Nav1.9 variant b; voltage-gated sodium channel Nav1.9 variant c; voltage-gated sodium channel NAV1.9b; voltage-gated sodium channel subunit alpha Nav1.9
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399119,582,829 - 119,654,522 (-)NCBIGRCm39mm39
GRCm39 Ensembl9119,582,825 - 119,654,522 (-)Ensembl
GRCm389119,753,763 - 119,825,456 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9119,753,759 - 119,825,456 (-)EnsemblGRCm38mm10GRCm38
MGSCv379119,662,881 - 119,734,574 (-)NCBIGRCm37mm9NCBIm37
MGSCv369119,602,461 - 119,672,558 (-)NCBImm8
Celera9120,223,700 - 120,294,696 (-)NCBICelera
Cytogenetic Map9F3NCBI
cM Map971.33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:9671787   PMID:10444332   PMID:10623609   PMID:11376006   PMID:12428758   PMID:12536125   PMID:14515348   PMID:15964986   PMID:16029194   PMID:16446141   PMID:16602821   PMID:16857712  
PMID:16985003   PMID:17167076   PMID:17363266   PMID:17513486   PMID:17911046   PMID:18096591   PMID:18270172   PMID:18280187   PMID:18399542   PMID:18498732   PMID:18498735   PMID:19146922  
PMID:19228393   PMID:19931571   PMID:20096094   PMID:20411123   PMID:21267068   PMID:21632935   PMID:21829440   PMID:21857998   PMID:21873635   PMID:22641814   PMID:22787056   PMID:22875929  
PMID:23238424   PMID:23575686   PMID:23596386   PMID:23643074   PMID:24036948   PMID:24440715   PMID:24719102   PMID:24972070   PMID:25101983   PMID:25369838   PMID:25385328   PMID:25959819  
PMID:26645915   PMID:26911685   PMID:27224030   PMID:27780178   PMID:28450535   PMID:28729444   PMID:29970412   PMID:30395542   PMID:30549873   PMID:30557356   PMID:31534133   PMID:31666509  
PMID:32325033   PMID:32817686  


Genomics

Comparative Map Data
Scn11a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399119,582,829 - 119,654,522 (-)NCBIGRCm39mm39
GRCm39 Ensembl9119,582,825 - 119,654,522 (-)Ensembl
GRCm389119,753,763 - 119,825,456 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9119,753,759 - 119,825,456 (-)EnsemblGRCm38mm10GRCm38
MGSCv379119,662,881 - 119,734,574 (-)NCBIGRCm37mm9NCBIm37
MGSCv369119,602,461 - 119,672,558 (-)NCBImm8
Celera9120,223,700 - 120,294,696 (-)NCBICelera
Cytogenetic Map9F3NCBI
cM Map971.33NCBI
SCN11A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl338,845,764 - 39,052,157 (-)EnsemblGRCh38hg38GRCh38
GRCh38338,845,764 - 39,051,944 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37338,887,255 - 39,093,435 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36338,862,264 - 38,967,056 (-)NCBINCBI36hg18NCBI36
Build 34338,862,263 - 38,967,056NCBI
Celera338,826,267 - 38,932,035 (-)NCBI
Cytogenetic Map3p22.2NCBI
HuRef338,929,417 - 39,033,960 (-)NCBIHuRef
CHM1_1338,838,871 - 38,946,272 (-)NCBICHM1_1
Scn11a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28119,495,550 - 119,567,044 (-)NCBI
Rnor_6.0 Ensembl8128,450,801 - 128,521,109 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08128,450,793 - 128,527,510 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08127,654,010 - 127,724,293 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48124,724,493 - 124,794,654 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18124,744,232 - 124,814,391 (-)NCBI
Celera8118,645,022 - 118,713,950 (-)NCBICelera
Cytogenetic Map8q32NCBI
Scn11a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542724,989,615 - 25,109,550 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542724,917,709 - 25,109,499 (+)NCBIChiLan1.0ChiLan1.0
SCN11A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1339,024,090 - 39,131,293 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl339,024,921 - 39,128,015 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0338,741,485 - 38,948,400 (-)NCBIMhudiblu_PPA_v0panPan3
SCN11A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1238,559,804 - 8,651,448 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl238,559,952 - 8,651,500 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha238,599,916 - 8,691,489 (-)NCBI
ROS_Cfam_1.0238,852,382 - 8,933,244 (-)NCBI
UMICH_Zoey_3.1238,662,540 - 8,754,003 (-)NCBI
UNSW_CanFamBas_1.0238,803,937 - 8,896,178 (-)NCBI
UU_Cfam_GSD_1.0238,797,979 - 8,889,539 (-)NCBI
Scn11a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118195,023,309 - 195,117,394 (-)NCBI
SpeTri2.0NW_00493647328,162,528 - 28,248,474 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCN11A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1323,602,977 - 23,692,220 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11323,602,378 - 23,692,281 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21325,889,505 - 25,951,832 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCN11A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.115466,295 - 575,460 (+)NCBI
ChlSab1.1 Ensembl15467,210 - 575,110 (+)Ensembl
Vero_WHO_p1.0NW_0236660639,093,710 - 9,305,205 (+)NCBI
Scn11a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247312,065,228 - 2,203,215 (+)NCBI

Position Markers
AF118044  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm389119,753,838 - 119,753,932UniSTSGRCm38
MGSCv379119,662,956 - 119,663,050UniSTSGRCm37
Celera9120,223,775 - 120,223,869UniSTS
Cytogenetic Map9F3-F4UniSTS
Whitehead/MRC_RH91179.85UniSTS
Scn11a  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm389119,753,862 - 119,754,283UniSTSGRCm38
MGSCv379119,662,896 - 119,663,189UniSTSGRCm37
MGSCv379119,663,201 - 119,663,303UniSTSGRCm37
Celera9120,223,799 - 120,224,220UniSTS
Cytogenetic Map9F3-F4UniSTS
cM Map971.0UniSTS
Scn11a  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm389119,753,778 - 119,754,071UniSTSGRCm38
MGSCv379119,662,896 - 119,663,189UniSTSGRCm37
Celera9120,223,715 - 120,224,008UniSTS
Cytogenetic Map9F3-F4UniSTS
cM Map971.0UniSTS
Scn11a  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm389119,754,083 - 119,754,185UniSTSGRCm38
MGSCv379119,663,201 - 119,663,303UniSTSGRCm37
Celera9120,224,020 - 120,224,122UniSTS
Cytogenetic Map9F3-F4UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4141833W10q13_mweight 10 weeks QTL 13 (mouse)Not determined63332429120362868Mouse
4141545Tailaq2_mtail length adjusted QTL 2 (mouse)Not determined63332429120362868Mouse
1357635Splq4_mspleen weight QTL 4 (mouse)Not determined963332429120362868Mouse
1300549Bbaa17_mB. burgdorferi-associated arthritis 17 (mouse)Not determined986230401120230530Mouse
1302103Dob2_mdietary obesity 2 (mouse)Not determined986239845120289624Mouse
11251716Siim2_mstress induced immobility 2 (mouse)986748483120748483Mouse
12880422V25Dq6_mvitamin D inactive form serum level QTL 6 (mouse)987800000121800000Mouse
10412242Alpq8_malcohol preference QTL 8 (mouse)Not determined989284925123284925Mouse
1301649Psl1_mpromotion susceptibility QTL 1 (mouse)Not determined989412277123412396Mouse
18182932Metl3_mmetabolite locus 3, N-acetylglutamate (mouse)989563342123563342Mouse
12910770Splic1_mspleen iron content 1 (mouse)991413879124595110Mouse
12910772Lvic6_mliver iron content 6 (mouse)991413879124595110Mouse
12910773Splic3_mspleen iron content 3 (mouse)991413879124595110Mouse
1558767Skmw11_mskeletal muscle weight 11 (mouse)Not determined991641084124595110Mouse
13463474Hbbcq5_mhemoglobin concentration QTL 5 (mouse)991641084124595110Mouse
13463475Hctq7_mhematocrit QTL 7 (mouse)991641084124595110Mouse
13463477Rbc9_mred blood cell count 9 (mouse)991641084124595110Mouse
13463478Mchq18_mmean corpuscular hemoglobin QTL 18 (mouse)991641084124595110Mouse
13463480Mchcq2_mmean corpuscular hemoglobin concentration QTL 2 (mouse)991641084124595110Mouse
12904937Edlmmq9_mextensor digitorum longus muscle mass QTL 9 (mouse)991683173124595110Mouse
12904947Tammq7_mtibialis anterior muscle mass QTL 7 (mouse)991683173124595110Mouse
12904961Gmmq7_mgastrocnemius muscle mass QTL 7 (mouse)991683173124595110Mouse
1302001Bdln5_mbody length 5 (mouse)Not determined993762590124595110Mouse
1301484Bwq6_mbody weight (mouse)Not determined993762590124595110Mouse
14746992Manh67_mmandible shape 67 (mouse)994036768124595110Mouse
11537364Cnes5_mC. neoformans susceptibility locus 5 (mouse)996917590124595110Mouse
1301297Lcho1_mliver cholesterol 1 (mouse)Not determined9101060861124595110Mouse
1357627Tgq2_mtriglyceride QTL 2 (mouse)Not determined9102000187124595110Mouse
1357648Obq18_mobesity QTL 18 (mouse)Not determined9102000187124595110Mouse
1301789Pbwg4_mpostnatal body weight growth 4 (mouse)Not determined9103289445124595110Mouse
10412290Pvacm1l_mplasma vascular cell adhesion molecule 1 levels (mouse)Not determined9103289445124595110Mouse
12879896Berr3_mberghei resistance locus 3 (mouse)9103289445124595110Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:194
Count of miRNA genes:148
Interacting mature miRNAs:169
Transcripts:ENSMUST00000070617
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000070617   ⟹   ENSMUSP00000065466
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl9119,753,763 - 119,825,456 (-)Ensembl
RefSeq Acc Id: ENSMUST00000215718   ⟹   ENSMUSP00000149420
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl9119,753,759 - 119,823,860 (-)Ensembl
RefSeq Acc Id: NM_011887   ⟹   NP_036017
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm399119,582,829 - 119,654,522 (-)NCBI
GRCm389119,753,763 - 119,825,456 (-)NCBI
MGSCv379119,662,881 - 119,734,574 (-)RGD
Celera9120,223,700 - 120,294,696 (-)RGD
cM Map9 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_017313362   ⟹   XP_017168851
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm399119,582,831 - 119,654,297 (-)NCBI
GRCm389119,753,768 - 119,825,231 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036017   ⟸   NM_011887
- UniProtKB: Q9R053 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017168851   ⟸   XM_017313362
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSMUSP00000065466   ⟸   ENSMUST00000070617
RefSeq Acc Id: ENSMUSP00000149420   ⟸   ENSMUST00000215718
Protein Domains
Ion_trans   Na_trans_assoc

Promoters
RGD ID:8671202
Promoter ID:EPDNEW_M13632
Type:initiation region
Name:Scn11a_1
Description:Mus musculus sodium channel, voltage-gated, type XI, alpha ,mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm389119,825,459 - 119,825,519EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1345149 AgrOrtholog
Ensembl Genes ENSMUSG00000034115 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000065466 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000149420 UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000070617 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000215718 UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.120.350 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Ion_trans_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_channel_a11su UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_channel_asu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_chnl_inactivation_gate UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_assoc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VGCC_Ca_Na UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:24046 UniProtKB/Swiss-Prot
MGD MGI:1345149 ENTREZGENE
NCBI Gene 24046 ENTREZGENE
PANTHER PTHR10037 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10037:SF210 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ion_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_assoc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Scn11a PhenoGen
PRINTS NACHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0R5RP39_MOUSE UniProtKB/TrEMBL
  A0A0R5RP40_MOUSE UniProtKB/TrEMBL
  A0A0R5RP42_MOUSE UniProtKB/TrEMBL
  Q9R053 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary E9QM88 UniProtKB/Swiss-Prot
  Q9JMD4 UniProtKB/Swiss-Prot